Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Srf

Cell type

Cell type Class
Others
Cell type
Cornea
MeSH Description
The transparent anterior portion of the fibrous coat of the eye consisting of five layers: stratified squamous CORNEAL EPITHELIUM; BOWMAN MEMBRANE; CORNEAL STROMA; DESCEMET MEMBRANE; and mesenchymal CORNEAL ENDOTHELIUM. It serves as the first refracting medium of the eye. It is structurally continuous with the SCLERA, avascular, receiving its nourishment by permeation through spaces between the lamellae, and is innervated by the ophthalmic division of the TRIGEMINAL NERVE via the ciliary nerves and those of the surrounding conjunctiva which together form plexuses. (Cline et al., Dictionary of Visual Science, 4th ed)

Attributes by original data submitter

Sample

source_name
cornea
tissue
whole cornea
age
~8 weeks
strain
mixed background
chip antibody
SRF (Santa Cruz Biotechnology, sc-335, Lot# I2712)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and SRF-DNA complexes were isolated with antibody. ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-300 bp) on an agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
40398680
Reads aligned (%)
88.1
Duplicates removed (%)
42.7
Number of peaks
20903 (qval < 1E-05)

mm9

Number of total reads
40398680
Reads aligned (%)
88.0
Duplicates removed (%)
42.8
Number of peaks
20896 (qval < 1E-05)

Base call quality data from DBCLS SRA